The detection of infective endocarditis (IE) of oral origin has been previously discussed. However, there are few reports confirming this infection using molecular biological techniques. We herein describe the case of a 67-year-old man who developed IE. Blood culture samples and strains obtained from the gingival and buccal mucosa showed 100% identity to Enterococcus faecalis JCM 5803 on sequencing of 16S rRNA gene fragments. A random amplification of polymorphic DNA (RAPD) analysis showed the same pattern for these samples, thus confirming the identity of E. faecalis isolates in the blood and oral mucosa. Our observations provide novel information regarding the level of identity between IE pathogens and oral bacteria.